Myelodysplastic SyndromesNCT04889729
GENOMED4ALL: Improving MDS Classification and Prognosis by AI
An observational study of Myelodysplastic Syndromes, run by Istituto Clinico Humanitas at 1 site in Italy.
Trial summary
Myelodysplastic syndromes (MDS) typically occur in elderly people. Current disese classifcation system and prognostic scores (International Prognostic Scoring System, IPSS) present limitations and in most cases fail to capture reliable prognostic information at individual level. Read more about this study
- Who is it for?
- Ages 18 years and older
- Conditions the study is for
- Myelodysplastic Syndromes
- How many people
- 13,284 participants
- Where
- 1 siteItaly
- Study dates
- 15 Mar 2021to 31 Dec 2024
- Phase
- Observational
- Are there results?
- None posted in the registry
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages 18 years and older
- All sexes
- No healthy volunteers
- Adult, Older adult
Study population: Patients affected by MDS. 13284 patients with clinical and genomic information availability
Who may be able to join
- Patients affected by MDS according WHO criteria > 18 years old
- Avaliability of clinical and hematological information
- Availability of information on targeted mutation screening
Who cannot join
- none of the above
Trial locations and contacts
1 site in 1 country.
About this study
Official title: Genomic and Personalized Medicine for All (GENOMED4ALL): Application of Artificial Intelligence to Improve Disease Classification and Prognosis in Myelodysplastic Syndrome.
Myelodysplastic syndromes (MDS) typically occur in elderly people. Current disese classifcation system and prognostic scores (International Prognostic Scoring System, IPSS) present limitations and in most cases fail to capture reliable prognostic information at individual level. Study of MDS has been rapidly transformed by genome characterization and there is increasing evidence that mutation screening may add significant information to currently available prognostic scores. The project will aim to develop artificial intelligence (AI)-based solutions to improve MDS classification and prognostication, through the implementation of a personalized medicine approach. In close collaboration with the European Reference Network on Rare Hematological Diseases (ERN-EuroBloodNet, FPA 739541), GENOMED4ALL involves multiple clinical partners from the network, while leveraging on healthcare information and repositories that will be gathered incorporating interoperability standards as promoted by ERN-EuroBloodNet central registry, the European Rare Blood Disorders Platform (ENROL, GA 947670).
Read the detailed description
Myelodysplastic syndromes (MDS) typically occur in elderly people. Patients present peripheral blood cytopenia, and with time a portion of these subjects evolve into acute myeloid leukaemia (AML). The natural history of MDS is heterogeneous ranging from conditions with a near-normal life expectancy to forms close to AML, and therefore a risk-adapted treatment strategy is mandatory. Current prognostic scores (Revised International Prognostic Scoring System, IPSS-R) present limitations, and in most cases fail to capture reliable prognostic information at individual level.
Study of MDS has been rapidly transformed by genome characterization. Somatic mutations occur in the genomes of hematopoietic stem cells at a low, but detectable frequency during normal DNA replication. Any genetic alteration that causes a selective advantage relative to other self-renewing cells will lead to clonal dominance (clonal haematopoiesis, CH). The consequence of CH is genomic instability leading to increased risk of acquiring additional mutations and to develop MDS, solid cancer and other illnesses. The time and place of individual mutations and their clonal emergence during the course of the disease are central issues for a better comprehension of MDS pathogenesis and phenotype and for the development of cancer preventive strategies.
Important steps forward have been made in defining the molecular architecture of MDS. The MDS associated with 5q deletion derives from the haploinsufficiency of RPS14 gene. Genes encoding for spliceosome components were identified in a high proportion of subjects with MDS. There is a close relationship between ring sideroblasts and SF3B1 mutations, which is consistent with a causal relationship. In addition, an increasing number of genes have been found to carry recurrent mutations in MDS, involved in DNA methylation (DNMT3A, TET2, IDH1/2), chromatin modification (EZH2, ASXL1), transcriptional regulation (RUNX1), signal transduction (KRAS, CBL).
Gene mutations have been reported to influence survival and risk of disease progression in MDS, and the evaluation of the mutation status may add significant information to currently used prognostic scores. For instance, we found that SF3B1 mutations were independent predictors of favorable prognosis, while driver mutations of ASXL1, SRSF2, RUNX1, TP53 and EZH2 genes were associated with a reduced probability of survival. MDS with ring sideroblasts provide the best evidence that the identification of the mutant gene responsible for the initial clone is relevant to clinical outcome. In fact, ring sideroblasts may be found not only in patients with a founding mutation in SF3B1, but also in those with an initiating oncogenic lesion in SRSF2. However, the median leukemia-free survival is >10 years in the former vs <2 years in the latter.
Moreover, mutation screening may affect clinical decision making : a) in MDS with 5q-, subjects carrying TP53 mutations have a higher risk of leukemic progression and a lower probability of response to lenalidomide; b) in patients receiving HSCT, TP53 mutations predict high probability of relapse; c) SF3B1 mutations are associated with increased probability of erythroid response to TGFb inhibitors (luspatercept), and d) TET2 mutations might be associated with response to HMA.
Despite these findings, caution is needed against immediately adopting such mutational testing in clinical practice. First, the presence of mutations in a given individual has only limited predictive power, as conversion to MDS is rare regardless of mutation status. In addition, in patients with overt MDS, genetic abnormalities explain only a proportion of the total hazard for survival associated with specific treatments, meaning that a large percentage is still associated with clinical and non-mutational factors. Comprehensive analyses of large patient population and new methods to study gene-gene interactions and genoptype-phenotype correlations are warranted to correctly estimate the independent effect of each genomic abnormality on clinical outcome and response to treatment.
By combining an already available, large amount of sequenced genomic data and clinical information, the authors hypothesize that AI will allow to understand better MDS biology and classification, enhance prognostic/predictive capacity of currently available tools and apply treatments in a more targeted way, thus facilitating the implementation of personalized medicine program across EU.
- Conditions
- Myelodysplastic Syndromes
- Keywords
- ARTIFICIAL INTELLIGENCE, HEMATOLOGICAL DISEASE, GENOMICS, PROGNOSIS, DISEASE CLASSIFICATION
- Medical subject headings
- Myelodysplastic Syndromes, Hematologic Diseases
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
| Study group | Role | What they receive |
|---|---|---|
| GENOMED4ALL - MDS patients | Information on targeted mutation screening (NGS including 60 genes related to MDS) from 13284 MDS patients |
What is being measured
The primary outcome is the main question the study is designed to answer.
Improving MDS classification
To improve classification of MDS by integrating clinical and hematological information with genomic features. To address this issue, different methods of statistical learning (Dirichlet processes (DP), Bayesian networks (BN)) and machine learning (deep learning physics informed neural network, constrained regression and deep models) will be compared in order to define specific genotype-phenotype correlations and to develop a new disease classification.
Measured: through study completion, an average of 2 years
Prediction of probability of overall survival (months between diagnosis and death or end of follow up) for patients with MDS
Overall survival (OS) will be defined as the time (expressed in months) between diagnosis and death (as a result of all causes) or end of follow-up (censored observations).
New prognostic scores will be defined including the following features: age expressed in years; sex (male or female); neutrophils count (number of neutrophils*10^6/L), platelets count (number of plateles 10^6/L), hemoglobin concentration (g/dl), cytogenetics (stratified according to IPPS-R criteria, Blood 2012 120: 2454-2465), percentage of bone marrrow blasts and presence of gene mutations (presence versus absence).
Different statistical methods will be used to measure prediction accuracy (measured by concordance index, C-index): Cox proporsional-hazard methods, random survival forests, neural networks, continous individualized risk index (CIRI), times series analysis and Markov modeling for stochastic trajectories prediction
Measured: through study completion, an average of 2 years
Prediction of probability of leukemia free surivival (months from diagnosis to progression to acute leukemia or end of follow up) for patients with MDS
Leukemia will be defined as the time (expressed in months) between diagnosis and progression to acute leukemia or end of follow-up.
New prognostic scores will be defined including the following features: age expressed in years; sex (male or female); neutrophils count (number of neutrophils*10^6/L), platelets count (number of plateles 10^6/L), hemoglobin concentration (g/dl), cytogenetics (stratified according to IPPS-R criteria, Blood 2012 120: 2454-2465), percentage of bone marrrow blasts and presence of gene mutations (presence versus absence).
Different statistical methods will be used to measure prediction accuracy (measured by concordance index, C-index): Cox proporsional-hazard methods, random survival forests, neural networks, continous individualized risk index (CIRI), times series analysis and Markov modeling for stochastic trajectories prediction
Measured: through study completion, an average of 2 years
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted17 May 2021
- Study start15 Mar 2021
- Primary completion15 Dec 2022 (estimated)
- Study completion31 Dec 2024 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Publications (33)Papers the sponsor has linked to this study.
- Other trials for Myelodysplastic SyndromesStudies of the same condition, open and under way.
- More trials run by Istituto Clinico HumanitasThe sponsor's other registered studies.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Observational
- Observational model
- Cohort
- Time perspective
- Retrospective
- Enrolment
- 13,284 participants (estimated)
Sponsor and investigators
- Lead sponsor
- Istituto Clinico Humanitas
- Sponsor type
- University, hospital or other
- Responsible party
- Sponsor
- Investigators
- Federico Alvarez, Principal investigator, UNIVERSIDAD POLITECNICA DE MADRID SPAINLucia Comnes, Principal investigator, DATAWIZARD SRL ITALYMar Manu Pereira, Principal investigator, FUNDACIO HOSPITAL UNIVERSITARI VALL D'HEBRON - INSTITUT DE RECERCA SPAINPierre Fenaux, Principal investigator, ASSISTANCE PUBLIQUE HOPITAUX DE PARIS FRANCETorsten Haferlach, Principal investigator, MLL MUNCHNER LEUKAMIELABOR GMBH GERMANYMaria Diez Campelo, Principal investigator, Instituto de investigacion biomedica de Salamanca, IBSAL SPAINUwe Platzbecker, Principal investigator, UNIVERSITAET LEIPZIG GERMANYGastone Castellani, Principal investigator, ALMA MATER STUDIORUM - UNIVERSITA DI BOLOGNA ITALY
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT04889729
- Sponsor's protocol ID
- GENOMED4ALL: MDS
- Status last verified
- Sep 2022
- First submitted
- 5 May 2021
- Last updated
- 9 Sep 2022
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
Publications
Bersanelli M, Travaglino E, Meggendorfer M, Matteuzzi T, Sala C, Mosca E, Chiereghin C, Di Nanni N, Gnocchi M, Zampini M, Rossi M, Maggioni G, Termanini A, Angelucci E, Bernardi M, Borin L, Bruno B, Bonifazi F, Santini V, Bacigalupo A, Voso MT, Oliva E, Riva M, Ubezio M, Morabito L, Campagna A, Saitta C, Savevski V, Giampieri E, Remondini D, Passamonti F, Ciceri F, Bolli N, Rambaldi A, Kern W, Kordasti S, Sole F, Palomo L, Sanz G, Santoro A, Platzbecker U, Fenaux P, Milanesi L, Haferlach T, Castellani G, Della Porta MG. Classification and Personalized Prognostic Assessment on the Basis of Clinical and Genomic Features in Myelodysplastic Syndromes. J Clin Oncol. 2021 Apr 10;39(11):1223-1233. doi: 10.1200/JCO.20.01659. Epub 2021 Feb 4.
PubMed 33539200Ades L, Itzykson R, Fenaux P. Myelodysplastic syndromes. Lancet. 2014 Jun 28;383(9936):2239-52. doi: 10.1016/S0140-6736(13)61901-7. Epub 2014 Mar 21.
PubMed 24656536Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, Bloomfield CD, Cazzola M, Vardiman JW. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016 May 19;127(20):2391-405. doi: 10.1182/blood-2016-03-643544. Epub 2016 Apr 11.
PubMed 27069254Della Porta MG, Travaglino E, Boveri E, Ponzoni M, Malcovati L, Papaemmanuil E, Rigolin GM, Pascutto C, Croci G, Gianelli U, Milani R, Ambaglio I, Elena C, Ubezio M, Da Via' MC, Bono E, Pietra D, Quaglia F, Bastia R, Ferretti V, Cuneo A, Morra E, Campbell PJ, Orazi A, Invernizzi R, Cazzola M; Rete Ematologica Lombarda (REL) Clinical Network. Minimal morphological criteria for defining bone marrow dysplasia: a basis for clinical implementation of WHO classification of myelodysplastic syndromes. Leukemia. 2015 Jan;29(1):66-75. doi: 10.1038/leu.2014.161. Epub 2014 May 20.
PubMed 24935723Senent L, Arenillas L, Luno E, Ruiz JC, Sanz G, Florensa L. Reproducibility of the World Health Organization 2008 criteria for myelodysplastic syndromes. Haematologica. 2013 Apr;98(4):568-75. doi: 10.3324/haematol.2012.071449. Epub 2012 Oct 12.
PubMed 23065505Malcovati L, Porta MG, Pascutto C, Invernizzi R, Boni M, Travaglino E, Passamonti F, Arcaini L, Maffioli M, Bernasconi P, Lazzarino M, Cazzola M. Prognostic factors and life expectancy in myelodysplastic syndromes classified according to WHO criteria: a basis for clinical decision making. J Clin Oncol. 2005 Oct 20;23(30):7594-603. doi: 10.1200/JCO.2005.01.7038. Epub 2005 Sep 26.
PubMed 16186598Malcovati L, Hellstrom-Lindberg E, Bowen D, Ades L, Cermak J, Del Canizo C, Della Porta MG, Fenaux P, Gattermann N, Germing U, Jansen JH, Mittelman M, Mufti G, Platzbecker U, Sanz GF, Selleslag D, Skov-Holm M, Stauder R, Symeonidis A, van de Loosdrecht AA, de Witte T, Cazzola M; European Leukemia Net. Diagnosis and treatment of primary myelodysplastic syndromes in adults: recommendations from the European LeukemiaNet. Blood. 2013 Oct 24;122(17):2943-64. doi: 10.1182/blood-2013-03-492884. Epub 2013 Aug 26.
PubMed 23980065Greenberg PL, Tuechler H, Schanz J, Sanz G, Garcia-Manero G, Sole F, Bennett JM, Bowen D, Fenaux P, Dreyfus F, Kantarjian H, Kuendgen A, Levis A, Malcovati L, Cazzola M, Cermak J, Fonatsch C, Le Beau MM, Slovak ML, Krieger O, Luebbert M, Maciejewski J, Magalhaes SM, Miyazaki Y, Pfeilstocker M, Sekeres M, Sperr WR, Stauder R, Tauro S, Valent P, Vallespi T, van de Loosdrecht AA, Germing U, Haase D. Revised international prognostic scoring system for myelodysplastic syndromes. Blood. 2012 Sep 20;120(12):2454-65. doi: 10.1182/blood-2012-03-420489. Epub 2012 Jun 27.
PubMed 22740453Della Porta MG, Tuechler H, Malcovati L, Schanz J, Sanz G, Garcia-Manero G, Sole F, Bennett JM, Bowen D, Fenaux P, Dreyfus F, Kantarjian H, Kuendgen A, Levis A, Cermak J, Fonatsch C, Le Beau MM, Slovak ML, Krieger O, Luebbert M, Maciejewski J, Magalhaes SM, Miyazaki Y, Pfeilstocker M, Sekeres MA, Sperr WR, Stauder R, Tauro S, Valent P, Vallespi T, van de Loosdrecht AA, Germing U, Haase D, Greenberg PL, Cazzola M. Validation of WHO classification-based Prognostic Scoring System (WPSS) for myelodysplastic syndromes and comparison with the revised International Prognostic Scoring System (IPSS-R). A study of the International Working Group for Prognosis in Myelodysplasia (IWG-PM). Leukemia. 2015 Jul;29(7):1502-13. doi: 10.1038/leu.2015.55. Epub 2015 Feb 27.
PubMed 25721895Cazzola M, Della Porta MG, Malcovati L. The genetic basis of myelodysplasia and its clinical relevance. Blood. 2013 Dec 12;122(25):4021-34. doi: 10.1182/blood-2013-09-381665. Epub 2013 Oct 17.
PubMed 24136165Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, Pellagatti A, Wainscoat JS, Hellstrom-Lindberg E, Gambacorti-Passerini C, Godfrey AL, Rapado I, Cvejic A, Rance R, McGee C, Ellis P, Mudie LJ, Stephens PJ, McLaren S, Massie CE, Tarpey PS, Varela I, Nik-Zainal S, Davies HR, Shlien A, Jones D, Raine K, Hinton J, Butler AP, Teague JW, Baxter EJ, Score J, Galli A, Della Porta MG, Travaglino E, Groves M, Tauro S, Munshi NC, Anderson KC, El-Naggar A, Fischer A, Mustonen V, Warren AJ, Cross NC, Green AR, Futreal PA, Stratton MR, Campbell PJ; Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med. 2011 Oct 13;365(15):1384-95. doi: 10.1056/NEJMoa1103283. Epub 2011 Sep 26.
PubMed 21995386Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G, Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F, Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature. 2011 Sep 11;478(7367):64-9. doi: 10.1038/nature10496.
PubMed 21909114Papaemmanuil E, Gerstung M, Malcovati L, Tauro S, Gundem G, Van Loo P, Yoon CJ, Ellis P, Wedge DC, Pellagatti A, Shlien A, Groves MJ, Forbes SA, Raine K, Hinton J, Mudie LJ, McLaren S, Hardy C, Latimer C, Della Porta MG, O'Meara S, Ambaglio I, Galli A, Butler AP, Walldin G, Teague JW, Quek L, Sternberg A, Gambacorti-Passerini C, Cross NC, Green AR, Boultwood J, Vyas P, Hellstrom-Lindberg E, Bowen D, Cazzola M, Stratton MR, Campbell PJ; Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium. Clinical and biological implications of driver mutations in myelodysplastic syndromes. Blood. 2013 Nov 21;122(22):3616-27; quiz 3699. doi: 10.1182/blood-2013-08-518886. Epub 2013 Sep 12.
PubMed 24030381Schanz J, Tuchler H, Sole F, Mallo M, Luno E, Cervera J, Granada I, Hildebrandt B, Slovak ML, Ohyashiki K, Steidl C, Fonatsch C, Pfeilstocker M, Nosslinger T, Valent P, Giagounidis A, Aul C, Lubbert M, Stauder R, Krieger O, Garcia-Manero G, Faderl S, Pierce S, Le Beau MM, Bennett JM, Greenberg P, Germing U, Haase D. New comprehensive cytogenetic scoring system for primary myelodysplastic syndromes (MDS) and oligoblastic acute myeloid leukemia after MDS derived from an international database merge. J Clin Oncol. 2012 Mar 10;30(8):820-9. doi: 10.1200/JCO.2011.35.6394. Epub 2012 Feb 13.
PubMed 22331955Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly P, Mudie L, McLaren S, O'Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Dohner K, Schlenk RF, Dohner H, Campbell PJ. Genomic Classification and Prognosis in Acute Myeloid Leukemia. N Engl J Med. 2016 Jun 9;374(23):2209-2221. doi: 10.1056/NEJMoa1516192.
PubMed 27276561
Study at a glance
From the registry record, last updated by the sponsor on 9 Sep 2022. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Genomic and Personalized Medicine for All (GENOMED4ALL): Application of Artificial Intelligence to Improve Disease Classification and Prognosis in Myelodysplastic Syndrome.
- ClinicalTrials.gov ID
- NCT04889729
- Acronym / sponsor ID
- GENOMED4ALL: MDS
- Conditions
- Myelodysplastic Syndromes
- Keywords
- ARTIFICIAL INTELLIGENCE, HEMATOLOGICAL DISEASE, GENOMICS, PROGNOSIS, DISEASE CLASSIFICATION
- Study type
- Observational
- Recruitment status
- Unknown status
- Enrolment
- 13,284 participants (estimated)
- Lead sponsor
- Istituto Clinico HumanitasUniversity, hospital or other
- Study start
- 15 Mar 2021 (actual)
- Primary completion
- 15 Dec 2022 (estimated)
- Study completion
- 31 Dec 2024 (estimated)
- First posted
- 17 May 2021 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
Myelodysplastic syndromes (MDS) typically occur in elderly people. Current disese classifcation system and prognostic scores (International Prognostic Scoring System, IPSS) present limitations and in most cases fail to capture reliable prognostic information at individual level. Study of MDS has been rapidly transformed by genome characterization and there is increasing evidence that mutation screening may add significant information to currently available prognostic scores. The project will aim to develop artificial intelligence (AI)-based solutions to improve MDS classification and prognostication, through the implementation of a personalized medicine approach. In close collaboration with the European Reference Network on Rare Hematological Diseases (ERN-EuroBloodNet, FPA 739541), GENOMED4ALL involves multiple clinical partners from the network, while leveraging on healthcare information and repositories that will be gathered incorporating interoperability standards as promoted by ERN-EuroBloodNet central registry, the European Rare Blood Disorders Platform (ENROL, GA 947670).
Detailed description
Myelodysplastic syndromes (MDS) typically occur in elderly people. Patients present peripheral blood cytopenia, and with time a portion of these subjects evolve into acute myeloid leukaemia (AML). The natural history of MDS is heterogeneous ranging from conditions with a near-normal life expectancy to forms close to AML, and therefore a risk-adapted treatment strategy is mandatory. Current prognostic scores (Revised International Prognostic Scoring System, IPSS-R) present limitations, and in most cases fail to capture reliable prognostic information at individual level.
Study of MDS has been rapidly transformed by genome characterization. Somatic mutations occur in the genomes of hematopoietic stem cells at a low, but detectable frequency during normal DNA replication. Any genetic alteration that causes a selective advantage relative to other self-renewing cells will lead to clonal dominance (clonal haematopoiesis, CH). The consequence of CH is genomic instability leading to increased risk of acquiring additional mutations and to develop MDS, solid cancer and other illnesses. The time and place of individual mutations and their clonal emergence during the course of the disease are central issues for a better comprehension of MDS pathogenesis and phenotype and for the development of cancer preventive strategies.
Important steps forward have been made in defining the molecular architecture of MDS. The MDS associated with 5q deletion derives from the haploinsufficiency of RPS14 gene. Genes encoding for spliceosome components were identified in a high proportion of subjects with MDS. There is a close relationship between ring sideroblasts and SF3B1 mutations, which is consistent with a causal relationship. In addition, an increasing number of genes have been found to carry recurrent mutations in MDS, involved in DNA methylation (DNMT3A, TET2, IDH1/2), chromatin modification (EZH2, ASXL1), transcriptional regulation (RUNX1), signal transduction (KRAS, CBL).
Gene mutations have been reported to influence survival and risk of disease progression in MDS, and the evaluation of the mutation status may add significant information to currently used prognostic scores. For instance, we found that SF3B1 mutations were independent predictors of favorable prognosis, while driver mutations of ASXL1, SRSF2, RUNX1, TP53 and EZH2 genes were associated with a reduced probability of survival. MDS with ring sideroblasts provide the best evidence that the identification of the mutant gene responsible for the initial clone is relevant to clinical outcome. In fact, ring sideroblasts may be found not only in patients with a founding mutation in SF3B1, but also in those with an initiating oncogenic lesion in SRSF2. However, the median leukemia-free survival is >10 years in the former vs <2 years in the latter.
Moreover, mutation screening may affect clinical decision making : a) in MDS with 5q-, subjects carrying TP53 mutations have a higher risk of leukemic progression and a lower probability of response to lenalidomide; b) in patients receiving HSCT, TP53 mutations predict high probability of relapse; c) SF3B1 mutations are associated with increased probability of erythroid response to TGFb inhibitors (luspatercept), and d) TET2 mutations might be associated with response to HMA.
Despite these findings, caution is needed against immediately adopting such mutational testing in clinical practice. First, the presence of mutations in a given individual has only limited predictive power, as conversion to MDS is rare regardless of mutation status. In addition, in patients with overt MDS, genetic abnormalities explain only a proportion of the total hazard for survival associated with specific treatments, meaning that a large percentage is still associated with clinical and non-mutational factors. Comprehensive analyses of large patient population and new methods to study gene-gene interactions and genoptype-phenotype correlations are warranted to correctly estimate the independent effect of each genomic abnormality on clinical outcome and response to treatment.
By combining an already available, large amount of sequenced genomic data and clinical information, the authors hypothesize that AI will allow to understand better MDS biology and classification, enhance prognostic/predictive capacity of currently available tools and apply treatments in a more targeted way, thus facilitating the implementation of personalized medicine program across EU.
Study design
- Observational model
- Cohort
- Time perspective
- Retrospective
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| GENOMED4ALL - MDS patients | – | –Information on targeted mutation screening (NGS including 60 genes related to MDS) from 13284 MDS patients |
Who may qualify
- Ages
- 18 years and older
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Adult, Older adult
- Study population
- Patients affected by MDS. 13284 patients with clinical and genomic information availability
Key inclusion criteria (3 listed)
- Patients affected by MDS according WHO criteria > 18 years old
- Avaliability of clinical and hematological information
- Availability of information on targeted mutation screening
Key exclusion criteria (1 listed)
- none of the above
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Primary outcome
Improving MDS classification
Time frame: through study completion, an average of 2 years
To improve classification of MDS by integrating clinical and hematological information with genomic features. To address this issue, different methods of statistical learning (Dirichlet processes (DP), Bayesian networks (BN)) and machine learning (deep learning physics informed neural network, constrained regression and deep models) will be compared in order to define specific genotype-phenotype correlations and to develop a new disease classification.
Prediction of probability of overall survival (months between diagnosis and death or end of follow up) for patients with MDS
Time frame: through study completion, an average of 2 years
Overall survival (OS) will be defined as the time (expressed in months) between diagnosis and death (as a result of all causes) or end of follow-up (censored observations). New prognostic scores will be defined including the following features: age expressed in years; sex (male or female); neutrophils count (number of neutrophils*10^6/L), platelets count (number of plateles 10^6/L), hemoglobin concentration (g/dl), cytogenetics (stratified according to IPPS-R criteria, Blood 2012 120: 2454-2465), percentage of bone marrrow blasts and presence of gene mutations (presence versus absence). Different statistical methods will be used to measure prediction accuracy (measured by concordance index, C-index): Cox proporsional-hazard methods, random survival forests, neural networks, continous individualized risk index (CIRI), times series analysis and Markov modeling for stochastic trajectories prediction
Prediction of probability of leukemia free surivival (months from diagnosis to progression to acute leukemia or end of follow up) for patients with MDS
Time frame: through study completion, an average of 2 years
Leukemia will be defined as the time (expressed in months) between diagnosis and progression to acute leukemia or end of follow-up. New prognostic scores will be defined including the following features: age expressed in years; sex (male or female); neutrophils count (number of neutrophils*10^6/L), platelets count (number of plateles 10^6/L), hemoglobin concentration (g/dl), cytogenetics (stratified according to IPPS-R criteria, Blood 2012 120: 2454-2465), percentage of bone marrrow blasts and presence of gene mutations (presence versus absence). Different statistical methods will be used to measure prediction accuracy (measured by concordance index, C-index): Cox proporsional-hazard methods, random survival forests, neural networks, continous individualized risk index (CIRI), times series analysis and Markov modeling for stochastic trajectories prediction
Results and safety
Results are not available in the source record.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 9 Sep 2022.
- Background: PubMed 33539200Bersanelli M, Travaglino E, Meggendorfer M, Matteuzzi T, Sala C, Mosca E, Chiereghin C, Di Nanni N, Gnocchi M, Zampini M, Rossi M, Maggioni G, Termanini A, Angelucci E, Bernardi M, Borin L, Bruno B, Bonifazi F, Santini V, Bacigalupo A, Voso MT, Oliva E, Riva M, Ubezio M, Morabito L, Campagna A, Saitta C, Savevski V, Giampieri E, Remondini D, Passamonti F, Ciceri F, Bolli N, Rambaldi A, Kern W, Kordasti S, Sole F, Palomo L, Sanz G, Santoro A, Platzbecker U, Fenaux P, Milanesi L, Haferlach T, Castellani G, Della Porta MG. Classification and Personalized Prognostic Assessment on the Basis of Clinical and Genomic Features in Myelodysplastic Syndromes. J Clin Oncol. 2021 Apr 10;39(11):1223-1233. doi: 10.1200/JCO.20.01659. Epub 2021 Feb 4.
- Background: PubMed 24656536Ades L, Itzykson R, Fenaux P. Myelodysplastic syndromes. Lancet. 2014 Jun 28;383(9936):2239-52. doi: 10.1016/S0140-6736(13)61901-7. Epub 2014 Mar 21.
- Background: PubMed 27069254Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, Bloomfield CD, Cazzola M, Vardiman JW. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016 May 19;127(20):2391-405. doi: 10.1182/blood-2016-03-643544. Epub 2016 Apr 11.
- Background: PubMed 24935723Della Porta MG, Travaglino E, Boveri E, Ponzoni M, Malcovati L, Papaemmanuil E, Rigolin GM, Pascutto C, Croci G, Gianelli U, Milani R, Ambaglio I, Elena C, Ubezio M, Da Via' MC, Bono E, Pietra D, Quaglia F, Bastia R, Ferretti V, Cuneo A, Morra E, Campbell PJ, Orazi A, Invernizzi R, Cazzola M; Rete Ematologica Lombarda (REL) Clinical Network. Minimal morphological criteria for defining bone marrow dysplasia: a basis for clinical implementation of WHO classification of myelodysplastic syndromes. Leukemia. 2015 Jan;29(1):66-75. doi: 10.1038/leu.2014.161. Epub 2014 May 20.
- Background: PubMed 23065505Senent L, Arenillas L, Luno E, Ruiz JC, Sanz G, Florensa L. Reproducibility of the World Health Organization 2008 criteria for myelodysplastic syndromes. Haematologica. 2013 Apr;98(4):568-75. doi: 10.3324/haematol.2012.071449. Epub 2012 Oct 12.
- Background: PubMed 16186598Malcovati L, Porta MG, Pascutto C, Invernizzi R, Boni M, Travaglino E, Passamonti F, Arcaini L, Maffioli M, Bernasconi P, Lazzarino M, Cazzola M. Prognostic factors and life expectancy in myelodysplastic syndromes classified according to WHO criteria: a basis for clinical decision making. J Clin Oncol. 2005 Oct 20;23(30):7594-603. doi: 10.1200/JCO.2005.01.7038. Epub 2005 Sep 26.
- Background: PubMed 23980065Malcovati L, Hellstrom-Lindberg E, Bowen D, Ades L, Cermak J, Del Canizo C, Della Porta MG, Fenaux P, Gattermann N, Germing U, Jansen JH, Mittelman M, Mufti G, Platzbecker U, Sanz GF, Selleslag D, Skov-Holm M, Stauder R, Symeonidis A, van de Loosdrecht AA, de Witte T, Cazzola M; European Leukemia Net. Diagnosis and treatment of primary myelodysplastic syndromes in adults: recommendations from the European LeukemiaNet. Blood. 2013 Oct 24;122(17):2943-64. doi: 10.1182/blood-2013-03-492884. Epub 2013 Aug 26.
- Background: PubMed 22740453Greenberg PL, Tuechler H, Schanz J, Sanz G, Garcia-Manero G, Sole F, Bennett JM, Bowen D, Fenaux P, Dreyfus F, Kantarjian H, Kuendgen A, Levis A, Malcovati L, Cazzola M, Cermak J, Fonatsch C, Le Beau MM, Slovak ML, Krieger O, Luebbert M, Maciejewski J, Magalhaes SM, Miyazaki Y, Pfeilstocker M, Sekeres M, Sperr WR, Stauder R, Tauro S, Valent P, Vallespi T, van de Loosdrecht AA, Germing U, Haase D. Revised international prognostic scoring system for myelodysplastic syndromes. Blood. 2012 Sep 20;120(12):2454-65. doi: 10.1182/blood-2012-03-420489. Epub 2012 Jun 27.
- Background: PubMed 25721895Della Porta MG, Tuechler H, Malcovati L, Schanz J, Sanz G, Garcia-Manero G, Sole F, Bennett JM, Bowen D, Fenaux P, Dreyfus F, Kantarjian H, Kuendgen A, Levis A, Cermak J, Fonatsch C, Le Beau MM, Slovak ML, Krieger O, Luebbert M, Maciejewski J, Magalhaes SM, Miyazaki Y, Pfeilstocker M, Sekeres MA, Sperr WR, Stauder R, Tauro S, Valent P, Vallespi T, van de Loosdrecht AA, Germing U, Haase D, Greenberg PL, Cazzola M. Validation of WHO classification-based Prognostic Scoring System (WPSS) for myelodysplastic syndromes and comparison with the revised International Prognostic Scoring System (IPSS-R). A study of the International Working Group for Prognosis in Myelodysplasia (IWG-PM). Leukemia. 2015 Jul;29(7):1502-13. doi: 10.1038/leu.2015.55. Epub 2015 Feb 27.
- Background: PubMed 24136165Cazzola M, Della Porta MG, Malcovati L. The genetic basis of myelodysplasia and its clinical relevance. Blood. 2013 Dec 12;122(25):4021-34. doi: 10.1182/blood-2013-09-381665. Epub 2013 Oct 17.
- Background: PubMed 21995386Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, Pellagatti A, Wainscoat JS, Hellstrom-Lindberg E, Gambacorti-Passerini C, Godfrey AL, Rapado I, Cvejic A, Rance R, McGee C, Ellis P, Mudie LJ, Stephens PJ, McLaren S, Massie CE, Tarpey PS, Varela I, Nik-Zainal S, Davies HR, Shlien A, Jones D, Raine K, Hinton J, Butler AP, Teague JW, Baxter EJ, Score J, Galli A, Della Porta MG, Travaglino E, Groves M, Tauro S, Munshi NC, Anderson KC, El-Naggar A, Fischer A, Mustonen V, Warren AJ, Cross NC, Green AR, Futreal PA, Stratton MR, Campbell PJ; Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med. 2011 Oct 13;365(15):1384-95. doi: 10.1056/NEJMoa1103283. Epub 2011 Sep 26.
- Background: PubMed 21909114Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G, Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F, Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature. 2011 Sep 11;478(7367):64-9. doi: 10.1038/nature10496.
Related trials for Myelodysplastic Syndromes
RecruitingObservational study
HPC Offered for PRESERVE Expansion
Bone Marrow Transplant (BMT)
RecruitingPhase 2
Haplo-identical Transplantation for Severe Aplastic Anemia, Hypo-plastic MDS and PNH Using Peripheral Blood Stem Cells and Post-transplant Cyclophosphamide for GVHD Prophylaxis
Severe Aplastic Anemia (SAA), Hypo-Plastic Myelodysplastic Syndrome (MDS)
RecruitingPhase 1/2
Pacritinib, a Kinase Inhibitor of CSF1R, IRAK1, JAK2, and FLT3, in Adults and Pediatric Participants 12 Years of Age or Older With Myelodysplastic Syndromes or Myelodysplastic/Myeloproliferative Neoplasms
Myelodysplastic Syndromes
RecruitingObservational study
Natural History of Trisomy 8-Associated Autoinflammatory Disease (TRIAD) and Related Disorders
Trisomy 8 Mosaicism, Trisomy 8 Associated Autoinflammatory Disease
RecruitingPhase 1
Autologous T Cells Transduced With Retroviral Vectors Expressing TCRs for Participant-specific Neoantigens in Patients With Hematologic Malignancies
Malignancy, Hematologic, Neoplasms, Hematologic
Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part. This study is not recruiting at the moment.
Federico Alvarez principal investigator
UNIVERSIDAD POLITECNICA DE MADRID SPAIN
Lucia Comnes principal investigator
DATAWIZARD SRL ITALY
Mar Manu Pereira principal investigator
FUNDACIO HOSPITAL UNIVERSITARI VALL D'HEBRON - INSTITUT DE RECERCA SPAIN
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
An observational study of Myelodysplastic Syndromes, run by Istituto Clinico Humanitas at 1 site in Italy.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 3 inclusion and 1 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: status not confirmed, as of the sponsor's last update on 9 Sep 2022. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in Italy. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
Results are not available in the source record.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Improving MDS classification (time frame: through study completion, an average of 2 years). The study lists 3 primary outcomes in all. It is what the study was designed to measure, not a finding.
Where can I read the original study information?
On the ClinicalTrials.gov record for NCT04889729, which also lists 33 linked publications.
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 9 Sep 2022.